TB-Profiler result

Run: SRR18213788
Summary

Run ID: SRR18213788

Sample name:

Date: 03-04-2023 19:29:24

Number of reads: 3971054

Percentage reads mapped: 99.63

Strain: lineage4.6.2.2

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.26
rpoB 759615 c.-192A>C upstream_gene_variant 0.12
rpoB 759620 c.-187A>C upstream_gene_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpR5 778298 c.-692C>T upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.14
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859904 p.Val172Gly missense_variant 0.13
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 0.99
rpoA 3878565 c.-58G>A upstream_gene_variant 0.14
ddn 3986997 p.Thr52Pro missense_variant 0.11
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 0.99
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0